breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-GLUT8-9_S24_L001_R2_001731,238109,903,158100.0%150.3 bases151 bases98.0%
errorsqtrim-GLUT8-9_S24_L001_R1_001731,428110,014,752100.0%150.4 bases151 bases99.7%
total1,462,666219,917,910100.0%150.4 bases151 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65246.71.398.3%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 100000971
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500047
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.86161

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Execution Times

stepstartendelapsed
Read and reference sequence file input22:35:44 02 Jan 201722:36:05 02 Jan 201721 seconds
Read alignment to reference genome22:36:06 02 Jan 201722:38:49 02 Jan 20172 minutes 43 seconds
Preprocessing alignments for candidate junction identification22:38:49 02 Jan 201722:39:27 02 Jan 201738 seconds
Preliminary analysis of coverage distribution22:39:27 02 Jan 201722:40:34 02 Jan 20171 minute 7 seconds
Identifying junction candidates22:40:34 02 Jan 201722:40:34 02 Jan 20170 seconds
Re-alignment to junction candidates22:40:34 02 Jan 201722:41:12 02 Jan 201738 seconds
Resolving alignments with junction candidates22:41:12 02 Jan 201722:42:14 02 Jan 20171 minute 2 seconds
Creating BAM files22:42:14 02 Jan 201722:43:06 02 Jan 201752 seconds
Tabulating error counts22:43:06 02 Jan 201722:44:04 02 Jan 201758 seconds
Re-calibrating base error rates22:44:04 02 Jan 201722:44:05 02 Jan 20171 second
Examining read alignment evidence22:44:05 02 Jan 201722:51:56 02 Jan 20177 minutes 51 seconds
Polymorphism statistics22:51:56 02 Jan 201722:51:56 02 Jan 20170 seconds
Output22:51:56 02 Jan 201722:52:09 02 Jan 201713 seconds
Total 16 minutes 24 seconds